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- PDB-7p2h: Dimethylated fusion protein of RSL and mussel adhesion peptide (M... -

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Basic information

Entry
Database: PDB / ID: 7p2h
TitleDimethylated fusion protein of RSL and mussel adhesion peptide (Mefp) in complex with cucurbit[7]uril, H3 sheet assembly
ComponentsFucose-binding lectin protein
KeywordsSUGAR BINDING PROTEIN / biomaterials / coiled coil / crystal engineering / IDP / macrocycle
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Lipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
cucurbit[7]uril / Fucose-binding lectin protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRamberg, K. / Engilberge, S. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation IrelandSSPC-PharM5 12/RC/2275_P2 Ireland
CitationJournal: Chemistry / Year: 2021
Title: Segregated Protein-Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons.
Authors: Ramberg, K.O. / Guagnini, F. / Engilberge, S. / Wronska, M.A. / Rennie, M.L. / Perez, J. / Crowley, P.B.
History
DepositionJul 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fucose-binding lectin protein
B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,20210
Polymers21,4622
Non-polymers2,7408
Water2,000111
1
A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules

A: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,30315
Polymers32,1923
Non-polymers4,11012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6170 Å2
ΔGint-17 kcal/mol
Surface area13380 Å2
MethodPISA
2
B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules

B: Fucose-binding lectin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,30315
Polymers32,1923
Non-polymers4,11012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6240 Å2
ΔGint-14 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.023, 51.023, 275.902
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-104-

NA

21B-104-

NA

31A-235-

HOH

41A-247-

HOH

51B-246-

HOH

61B-254-

HOH

71B-258-

HOH

81B-261-

HOH

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Components

#1: Protein Fucose-binding lectin protein / Putative fucose-binding lectin protein


Mass: 10730.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria)
Gene: E7Z57_08365, HXP36_18875, RSP795_21825, RSP822_19650, RUN39_v1_50103
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4TLR1
#2: Chemical ChemComp-QQ7 / cucurbit[7]uril


Mass: 1162.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H42N28O14 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15 % PEG 10000 0.1 M Bis-Tris pH 5.5 0.2 M MgCl2 4 mM Q7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.149→43.63 Å / Num. obs: 14627 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 37.38 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.035 / Rsym value: 0.112 / Net I/σ(I): 12.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 733 / CC1/2: 0.9 / Rpim(I) all: 0.313 / Rrim(I) all: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BT9

2bt9


Resolution: 2.15→43.63 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2.86 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 721 4.94 %
Rwork0.1813 13882 -
obs0.1831 14603 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.87 Å2 / Biso mean: 43.721 Å2 / Biso min: 28.54 Å2
Refinement stepCycle: final / Resolution: 2.15→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1382 0 194 111 1687
Biso mean--44.06 46.11 -
Num. residues----179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.310.30221530.267527782931
2.31-2.550.30061560.235227732929
2.55-2.910.25421190.209427662885
2.92-3.670.21381580.178127802938
3.67-43.630.17051350.147827852920

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